[gmx-users] REMD-error

[Bratin Kumar Das]

Respected Mark Abraham,
                                          The command-line and the job
submission script is given below

#!/bin/bash
#SBATCH -n 130 # Number of cores
#SBATCH -N 5   # no of nodes
#SBATCH -t 0-20:00:00 # Runtime in D-HH:MM
#SBATCH -p cpu # Partition to submit to
#SBATCH -o hostname_%j.out # File to which STDOUT will be written
#SBATCH -e hostname_%j.err # File to which STDERR will be written
#loading gromacs
module load gromacs/2018.4
#specifying work_dir
WORKDIR=/home/chm_bratin/GMX_Projects/REMD/4wbu-REMD-inst-clust_1/stage-1


mpirun -np 130 gmx_mpi_d mdrun -v -s remd_nvt_next2.tpr -multidir equil0
equil1 equil2 equil3 equil4 equil5 equil6 equil7 equil8 equil9 equil10
equil11 equil12 equil13 equil14 equil15 equil16 equil17 equil18 equil19
equil20 equil21 equil22 equil23 equil24 equil25 equil26 equil27 equil28
equil29 equil30 equil31 equil32 equil33 equil34 equil35 equil36 equil37
equil38 equil39 equil40 equil41 equil42 equil43 equil44 equil45 equil46
equil47 equil48 equil49 equil50 equil51 equil52 equil53 equil54 equil55
equil56 equil57 equil58 equil59 equil60 equil61 equil62 equil63 equil64
-deffnm remd_nvt -cpi remd_nvt.cpt -append

On Wed, Sep 4, 2019 at 2:13 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> We need to see your command line in order to have a chance of helping.
>
> Mark
>
> On Wed, 4 Sep 2019 at 05:46, Bratin Kumar Das <177cy500.bratin at nitk.edu.in
> >
> wrote:
>
> > Dear all,
> >             I am running one REMD simulation with 65 replicas. I am using
> > 130 cores for the simulation. I am getting the following error.
> >
> > Fatal error:
> > Your choice of number of MPI ranks and amount of resources results in
> using
> > 16
> > OpenMP threads per rank, which is most likely inefficient. The optimum is
> > usually between 1 and 6 threads per rank. If you want to run with this
> > setup,
> > specify the -ntomp option. But we suggest to change the number of MPI
> > ranks.
> >
> > when I am using -ntomp option ...it is throwing another error
> >
> > Fatal error:
> > Setting the number of thread-MPI ranks is only supported with thread-MPI
> > and
> > GROMACS was compiled without thread-MPI
> >
> >
> > while GROMACS is compiled with threated-MPI...
> >
> > plerase help me in this regard.
> > --
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